# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 01:16:44 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-phenyl-4-[[(3~{S})-piperidin-3-yl]amino]-1~{H}-indole-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(N[C@H]2CCCNC2)c3cc([nH]c13)c4ccccc4
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 D4Z  D4Z  2-phenyl-4-[[(3~{S})-piperidin-3-yl]amino]-1~{H}-indole-7-carboxamide  ligand  47  25  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D4Z
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 D4Z  C2   C  C     0   0.509   1.2309  -3.7667  -0.1321
 D4Z  C7   C  CR6   0   0.325  -1.4043  -0.3260   0.3620
 D4Z  C9   C  CH1   0  -0.092  -3.6285   0.7765   0.4209
 D4Z  C11  C  CH2   0  -0.452  -4.1788   2.0842   0.9806
 D4Z  C12  C  CH2   0  -0.447  -5.6962   2.1377   0.8307
 D4Z  C13  C  CH2   0  -0.313  -6.1065   1.8749  -0.6154
 D4Z  C15  C  CH2   0  -0.309  -4.1163   0.5820  -1.0229
 D4Z  C16  C  CR56  0  -0.012  -0.0062  -0.1791   0.2143
 D4Z  C21  C  CR56  0   0.334   0.8172  -1.3107   0.0724
 D4Z  C22  C  CR6   0   0.064   3.3755   1.2601  -0.0508
 D4Z  C24  C  CR16  0  -0.234   4.5246   3.3681  -0.3564
 D4Z  C27  C  CR16  0  -0.317   4.6143   0.6441   0.1440
 D4Z  N1   N  NH2   0  -0.830   0.6960  -4.9959  -0.2387
 D4Z  O3   O  O     0  -0.512   2.4517  -3.5975  -0.1825
 D4Z  C4   C  CR6   0  -0.122   0.3141  -2.6282   0.0528
 D4Z  C5   C  CR16  0  -0.321  -1.0626  -2.7332   0.2220
 D4Z  C6   C  CR16  0  -0.375  -1.9035  -1.6347   0.3721
 D4Z  N14  N  NH1   0  -0.578  -5.5588   0.6443  -1.1646
 D4Z  C17  C  CR15  0  -0.451   0.8426   0.9643   0.1774
 D4Z  C18  C  CR5   0   0.374   2.1270   0.5093   0.0188
 D4Z  N19  N  NR15  0  -0.755   2.0933  -0.8620  -0.0415
 D4Z  C23  C  CR16  0  -0.331   3.3513   2.6348  -0.3061
 D4Z  C25  C  CR16  0  -0.269   5.7517   2.7443  -0.1634
 D4Z  C26  C  CR16  0  -0.237   5.7892   1.3795   0.0855
 D4Z  H1   H  HCH1  0   0.236  -4.0202  -0.0425   1.0346
 D4Z  H2   H  HCH2  0   0.246  -3.8886   2.1956   2.0280
 D4Z  H3   H  HCH2  0   0.221  -3.7305   2.9236   0.4349
 D4Z  H4   H  HCH2  0   0.219  -6.1563   1.3873   1.4822
 D4Z  H5   H  HCH2  0   0.233  -6.0725   3.1099   1.1581
 D4Z  H6   H  HCH2  0   0.237  -7.1940   1.8438  -0.7062
 D4Z  H7   H  HCH2  0   0.215  -5.7613   2.7052  -1.2419
 D4Z  H8   H  HCH2  0   0.217  -3.6713   1.3687  -1.6435
 D4Z  H9   H  HCH2  0   0.241  -3.7618  -0.3716  -1.4215
 D4Z  H10  H  HCR6  0   0.260   4.4812   4.4313  -0.5537
 D4Z  H11  H  HCR6  0   0.246   4.6788  -0.4150   0.3597
 D4Z  H12  H  HNH2  0   0.401   1.3006  -5.7804  -0.4170
 D4Z  H13  H  HNH2  0   0.410  -0.2912  -5.1612  -0.3141
 D4Z  H14  H  HCR6  0   0.242  -1.5377  -3.7060   0.2484
 D4Z  H15  H  HCR6  0   0.262  -2.9624  -1.8143   0.4939
 D4Z  H16  H  HNH1  0   0.386  -1.7432   1.6601   0.3244
 D4Z  H17  H  HNH1  0   0.341  -5.9757  -0.1485  -0.6901
 D4Z  H19  H  HCR5  0   0.253   0.5538   1.9980   0.2871
 D4Z  H20  H  HNR5  0   0.410   2.8716  -1.4853  -0.1849
 D4Z  H21  H  HCR6  0   0.253   2.4064   3.1345  -0.4781
 D4Z  H22  H  HCR6  0   0.259   6.6683   3.3175  -0.2087
 D4Z  H23  H  HCR6  0   0.260   6.7369   0.8813   0.2429
 D4Z  N8   N  NH1   0  -0.697  -2.1844   0.7742   0.5169

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 D4Z  C13  N14  single    1.455  0.020  1.455
 D4Z  C13  C12  single    1.526  0.020  1.526
 D4Z  C24  C25  aromatic  1.390  0.020  1.390
 D4Z  C24  C23  aromatic  1.385  0.020  1.385
 D4Z  N14  C15  single    1.451  0.020  1.451
 D4Z  C12  C11  single    1.526  0.020  1.526
 D4Z  C25  C26  aromatic  1.388  0.020  1.388
 D4Z  C23  C22  aromatic  1.398  0.020  1.398
 D4Z  C11  C9   single    1.525  0.020  1.525
 D4Z  C15  C9   single    1.536  0.020  1.536
 D4Z  C26  C27  aromatic  1.387  0.020  1.387
 D4Z  C9   N8   single    1.447  0.020  1.447
 D4Z  C22  C27  aromatic  1.397  0.020  1.397
 D4Z  C22  C18  single    1.459  0.020  1.459
 D4Z  C17  C18  aromatic  1.372  0.020  1.372
 D4Z  C17  C16  aromatic  1.424  0.020  1.424
 D4Z  N8   C7   single    1.358  0.020  1.358
 D4Z  C18  N19  aromatic  1.373  0.020  1.373
 D4Z  C16  C7   aromatic  1.414  0.020  1.414
 D4Z  C16  C21  aromatic  1.407  0.020  1.407
 D4Z  C7   C6   aromatic  1.401  0.020  1.401
 D4Z  N19  C21  aromatic  1.358  0.020  1.358
 D4Z  C21  C4   aromatic  1.410  0.020  1.410
 D4Z  C6   C5   aromatic  1.392  0.020  1.392
 D4Z  C4   C5   aromatic  1.391  0.020  1.391
 D4Z  C4   C2   single    1.473  0.020  1.473
 D4Z  O3   C2   double    1.234  0.020  1.234
 D4Z  C2   N1   single    1.345  0.020  1.345
 D4Z  C9   H1   single    0.970  0.020  1.090
 D4Z  C11  H2   single    0.970  0.020  1.090
 D4Z  C11  H3   single    0.970  0.020  1.090
 D4Z  C12  H4   single    0.970  0.020  1.090
 D4Z  C12  H5   single    0.970  0.020  1.090
 D4Z  C13  H6   single    0.970  0.020  1.090
 D4Z  C13  H7   single    0.970  0.020  1.090
 D4Z  C15  H8   single    0.970  0.020  1.090
 D4Z  C15  H9   single    0.970  0.020  1.090
 D4Z  C24  H10  single    0.930  0.020  1.080
 D4Z  C27  H11  single    0.930  0.020  1.080
 D4Z  N1   H12  single    0.860  0.020  1.020
 D4Z  N1   H13  single    0.860  0.020  1.020
 D4Z  C5   H14  single    0.930  0.020  1.080
 D4Z  C6   H15  single    0.930  0.020  1.080
 D4Z  N8   H16  single    0.890  0.020  1.040
 D4Z  N14  H17  single    0.890  0.020  1.040
 D4Z  C17  H19  single    0.930  0.020  1.080
 D4Z  N19  H20  single    0.860  0.020  1.020
 D4Z  C23  H21  single    0.930  0.020  1.080
 D4Z  C25  H22  single    0.930  0.020  1.080
 D4Z  C26  H23  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 D4Z  C4   C2   O3   120.99  3.000
 D4Z  O3   C2   N1   121.05  3.000
 D4Z  C4   C2   N1   117.96  3.000
 D4Z  N8   C7   C6   123.48  3.000
 D4Z  C6   C7   C16  116.77  3.000
 D4Z  N8   C7   C16  119.74  3.000
 D4Z  H1   C9   N8   108.57  3.000
 D4Z  H1   C9   C15  108.55  3.000
 D4Z  N8   C9   C15  112.27  3.000
 D4Z  H1   C9   C11  107.84  3.000
 D4Z  N8   C9   C11  109.69  3.000
 D4Z  C15  C9   C11  109.80  3.000
 D4Z  H3   C11  H2   106.88  3.000
 D4Z  H3   C11  C12  109.31  3.000
 D4Z  H2   C11  C12  110.78  3.000
 D4Z  H3   C11  C9   109.03  3.000
 D4Z  H2   C11  C9   110.08  3.000
 D4Z  C12  C11  C9   110.66  3.000
 D4Z  H5   C12  H4   106.66  3.000
 D4Z  H5   C12  C13  110.15  3.000
 D4Z  H4   C12  C13  109.44  3.000
 D4Z  H5   C12  C11  110.13  3.000
 D4Z  H4   C12  C11  109.60  3.000
 D4Z  C13  C12  C11  110.76  3.000
 D4Z  H7   C13  H6   106.73  3.000
 D4Z  H7   C13  N14  107.85  3.000
 D4Z  H6   C13  N14  108.63  3.000
 D4Z  H7   C13  C12  109.07  3.000
 D4Z  H6   C13  C12  110.58  3.000
 D4Z  N14  C13  C12  113.72  3.000
 D4Z  H9   C15  H8   106.74  3.000
 D4Z  H9   C15  N14  108.93  3.000
 D4Z  H8   C15  N14  108.52  3.000
 D4Z  H9   C15  C9   110.50  3.000
 D4Z  H8   C15  C9   108.19  3.000
 D4Z  N14  C15  C9   113.71  3.000
 D4Z  C17  C16  C21  107.12  3.000
 D4Z  C21  C16  C7   120.39  3.000
 D4Z  C17  C16  C7   132.49  3.000
 D4Z  N19  C21  C4   130.01  3.000
 D4Z  C4   C21  C16  122.97  3.000
 D4Z  N19  C21  C16  107.03  3.000
 D4Z  C23  C22  C18  120.00  3.000
 D4Z  C18  C22  C27  121.69  3.000
 D4Z  C23  C22  C27  118.31  3.000
 D4Z  H10  C24  C25  120.10  3.000
 D4Z  H10  C24  C23  119.54  3.000
 D4Z  C25  C24  C23  120.36  3.000
 D4Z  H11  C27  C26  118.46  3.000
 D4Z  H11  C27  C22  120.79  3.000
 D4Z  C26  C27  C22  120.75  3.000
 D4Z  H13  N1   H12  116.70  3.000
 D4Z  H13  N1   C2   123.21  3.000
 D4Z  H12  N1   C2   119.18  3.000
 D4Z  C5   C4   C21  114.95  3.000
 D4Z  C5   C4   C2   124.94  3.000
 D4Z  C21  C4   C2   120.11  3.000
 D4Z  H14  C5   C6   116.19  3.000
 D4Z  H14  C5   C4   120.33  3.000
 D4Z  C6   C5   C4   123.48  3.000
 D4Z  H15  C6   C5   118.23  3.000
 D4Z  H15  C6   C7   120.34  3.000
 D4Z  C5   C6   C7   121.43  3.000
 D4Z  H17  N14  C15  109.25  3.000
 D4Z  H17  N14  C13  109.27  3.000
 D4Z  C15  N14  C13  111.95  3.000
 D4Z  H19  C17  C18  125.47  3.000
 D4Z  H19  C17  C16  127.37  3.000
 D4Z  C18  C17  C16  107.13  3.000
 D4Z  N19  C18  C17  108.27  3.000
 D4Z  N19  C18  C22  122.21  3.000
 D4Z  C17  C18  C22  129.51  3.000
 D4Z  H20  N19  C18  127.25  3.000
 D4Z  H20  N19  C21  122.25  3.000
 D4Z  C18  N19  C21  110.46  3.000
 D4Z  H21  C23  C24  119.30  3.000
 D4Z  H21  C23  C22  119.86  3.000
 D4Z  C24  C23  C22  120.84  3.000
 D4Z  H22  C25  C26  120.37  3.000
 D4Z  H22  C25  C24  120.28  3.000
 D4Z  C26  C25  C24  119.35  3.000
 D4Z  H23  C26  C25  120.16  3.000
 D4Z  H23  C26  C27  119.44  3.000
 D4Z  C25  C26  C27  120.40  3.000
 D4Z  H16  N8   C9   115.00  3.000
 D4Z  H16  N8   C7   116.03  3.000
 D4Z  C9   N8   C7   124.54  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 D4Z  CONST_01  C18  C17  C16  C7   180.00   0.0  0
 D4Z  CONST_02  N19  C21  C16  C7   180.00   0.0  0
 D4Z  CONST_03  C4   C21  C16  C7     0.00   0.0  0
 D4Z  CONST_04  C4   C5   C6   C7     0.00   0.0  0
 D4Z  CONST_05  C22  C18  C17  C16  180.00   0.0  0
 D4Z  CONST_06  N19  C18  C17  C16    0.00   0.0  0
 D4Z  CONST_07  C5   C6   C7   C16    0.00   0.0  0
 D4Z  CONST_08  C18  N19  C21  C16    0.00   0.0  0
 D4Z  CONST_09  C5   C4   C21  C16    0.00   0.0  0
 D4Z  CONST_10  C18  C17  C16  C21    0.00   0.0  0
 D4Z  CONST_11  C6   C7   C16  C21    0.00   0.0  0
 D4Z  CONST_12  C22  C18  N19  C21  180.00   0.0  0
 D4Z  CONST_13  C17  C18  N19  C21    0.00   0.0  0
 D4Z  CONST_14  C6   C5   C4   C21    0.00   0.0  0
 D4Z  CONST_15  C25  C24  C23  C22    0.00   0.0  0
 D4Z  CONST_16  C25  C26  C27  C22    0.00   0.0  0
 D4Z  CONST_17  C27  C26  C25  C24    0.00   0.0  0
 D4Z  CONST_18  C27  C22  C23  C24    0.00   0.0  0
 D4Z  CONST_19  C18  C22  C23  C24  180.00   0.0  0
 D4Z  CONST_22  C17  C16  C21  C4   180.00   0.0  0
 D4Z  CONST_23  C18  N19  C21  C4   180.00   0.0  0
 D4Z  CONST_24  N19  C21  C4   C5   180.00   0.0  0
 D4Z  CONST_25  C17  C16  C7   C6   180.00   0.0  0
 D4Z  CONST_27  N19  C21  C16  C17    0.00   0.0  0
 D4Z  CONST_28  C26  C27  C22  C18  180.00   0.0  0
 D4Z  CONST_30  C26  C25  C24  C23    0.00   0.0  0
 D4Z  CONST_31  C26  C27  C22  C23    0.00   0.0  0
 D4Z  CONST_32  C16  C21  C4   C2   180.00   0.0  0
 D4Z  CONST_33  N19  C21  C4   C2     0.00   0.0  0
 D4Z  CONST_34  C6   C5   C4   C2   180.00   0.0  0
 D4Z  CONST_35  N8   C7   C16  C21  180.00   0.0  0
 D4Z  CONST_36  N8   C7   C6   C5   180.00   0.0  0
 D4Z  CONST_37  C17  C16  C7   N8     0.00   0.0  0
 D4Z  CONST_38  C16  C7   N8   C9   180.00   0.0  0
 D4Z  CONST_39  C6   C7   N8   C9     0.00   0.0  0
 D4Z  CONST_40  H19  C17  C16  C7     0.00   0.0  0
 D4Z  CONST_41  H14  C5   C6   C7   180.00   0.0  0
 D4Z  CONST_42  H15  C6   C7   C16  180.00   0.0  0
 D4Z  CONST_43  H20  N19  C21  C16  180.00   0.0  0
 D4Z  CONST_44  H10  C24  C23  C22  180.00   0.0  0
 D4Z  CONST_45  H23  C26  C27  C22  180.00   0.0  0
 D4Z  CONST_46  H22  C25  C26  C27  180.00   0.0  0
 D4Z  CONST_47  H21  C23  C22  C27  180.00   0.0  0
 D4Z  CONST_48  H11  C27  C22  C18    0.00   0.0  0
 D4Z  CONST_49  H16  N8   C7   C16    0.00   0.0  0
 D4Z  CONST_50  H12  N1   C2   C4   180.00   0.0  0
 D4Z  CONST_51  H13  N1   C2   C4     0.00   0.0  0
 D4Z  Var_01    C13  C12  C11  C9   -53.26  30.0  1
 D4Z  Var_02    C13  N14  C15  C9    54.55  30.0  1
 D4Z  Var_03    N14  C13  C12  C11   53.47  30.0  1
 D4Z  Var_04    C15  N14  C13  C12  -53.69  30.0  1
 D4Z  Var_05    O3   C2   C4   C21    4.88  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 D4Z  chir_01  C9  C11  C15  N8  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 D4Z  plan-1  C22  0.020
 D4Z  plan-1  C24  0.020
 D4Z  plan-1  C27  0.020
 D4Z  plan-1  C18  0.020
 D4Z  plan-1  C23  0.020
 D4Z  plan-1  C25  0.020
 D4Z  plan-1  C26  0.020
 D4Z  plan-1  H10  0.020
 D4Z  plan-1  H11  0.020
 D4Z  plan-1  H21  0.020
 D4Z  plan-1  H22  0.020
 D4Z  plan-1  H23  0.020
 D4Z  plan-2  C2   0.020
 D4Z  plan-2  C7   0.020
 D4Z  plan-2  C16  0.020
 D4Z  plan-2  C21  0.020
 D4Z  plan-2  C22  0.020
 D4Z  plan-2  C4   0.020
 D4Z  plan-2  C5   0.020
 D4Z  plan-2  C6   0.020
 D4Z  plan-2  C17  0.020
 D4Z  plan-2  C18  0.020
 D4Z  plan-2  N19  0.020
 D4Z  plan-2  H14  0.020
 D4Z  plan-2  H15  0.020
 D4Z  plan-2  H19  0.020
 D4Z  plan-2  H20  0.020
 D4Z  plan-2  N8   0.020
 D4Z  plan-3  C7   0.020
 D4Z  plan-3  C9   0.020
 D4Z  plan-3  H16  0.020
 D4Z  plan-3  N8   0.020
 D4Z  plan-4  C2   0.020
 D4Z  plan-4  N1   0.020
 D4Z  plan-4  O3   0.020
 D4Z  plan-4  C4   0.020
 D4Z  plan-4  H12  0.020
 D4Z  plan-4  H13  0.020

